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Quick Start: Yeast Display

This section describes the steps for planning a three-round yeast display selection experiment following Gabe Rocklin's massively parallel measurement of protein stability.

It is best to run this initially on a local Dockerized instance of Aquarium. If you haven't done so already, you can find steps for installing a Dockerized Aquarium instance here.

You will need to download and install three workflow libraries. You can find instructions for installing workflows here. It is a good idea to backup the database before importing, using the script hot_swap_db.py. The libraries are:

It is also a good idea to back up the database (using a distinct file name) after importing these.

Next, you will need to populate the database with some Samples. To do this, open the VS Code terminal using ^~ and run

python util/load_test_samples.py -f yeast_display_test_samples.json

From the browser, you should see that the following Samples are loaded:

►	8: SDO + 2% Galactose -His -Trp -Ura		
►	7: SDO -His -Trp -Ura		
►	6: Anti-c-myc-FITC		
►	5: Chymotrypsin		
►	4: Trypsin		
►	3: AMA1-best		
►	2: EBY100 + PETCONv3_baker		
►	1: DNA LIBRARY SAMPLE NAME

You can again back up the database (using a third distinct file name) after creating these.

Next, from the VS Code terminal, run:

vscode@docker-desktop:/workspaces/menagerie$ python plan_protein_stability.py -t

Which produces the output:

RUNNING IN TEST MODE
Connected to Aquarium at http://localhost/ using pydent version 0.0.35
Logged in as Joe Neptune

Set IO for Innoculate Yeast Library
### 1 total operations

Planning innoculation of library on 2020-03-06
Set IO for Store Yeast Library Sample
### 2 total operations

Set IO for Dilute Yeast Library
### 3 total operations

Trypsin 0
Set IO for Challenge and Label
Set IO for Sort Yeast Display Library
Set IO for Innoculate Yeast Library
Set IO for Store Yeast Library Sample
### 7 total operations
.
.
.
Created Plan: http://localhost//plans?plan_id=1
103 total operations.
96 total wires.

You may also see warnings like these near the beginning of the output:

WARNING: Sample not found: SDO -His -Trp -Ura
WARNING: ObjectType not found: Yeast Library Glycerol Stock

This is probably fine as it is likely the result of the software looking for Samples and ObjectTypes listed in aquarium_defaults.json that are not in the minimal database that has been set up.

When you click on the link to the plan, you should see this: Yeast Display Plan

Note that the Plan will not be ready to launch, because there are no Items in the Aquarium inventory.